Genome wide association studies contributed to a better understanding of the etiology of inflammatory bowel disease (IBD). While over 240 genetic associations with IBD have since been identified, functional follow-up studies are still in their infancy with the overall pathogenesis of IBD remaining unsolved. E.g., a functional understanding of the genetic association between the human leukocyte antigen (HLA) region and ulcerative colitis (UC) – one subtypes of IBD – is still lacking. Here, we analyzed whether an autoimmune reaction involving the HLA class II proteins HLA-DQ and -DR, both being strongly associated with UC, could be a disease trigger or driver. To this end, genotype data derived from whole exome sequencing and genome-wide SNP array data of 863 German UC patients as well as 4,185 healthy controls were analyzed. Association analyses identified novel variants in the NOD2 and SNX20 genes to be linked with UC and confirmed known HLA allele associations. Employing the genetic data, we generated patient-specific self-immunopeptidomes and in silico predicted HLA-peptide binding. Peptidome-wide association analyses of peptide binding preferences in a set of candidate proteins yielded significant associations with 234 specific peptides. Interestingly, none of those peptides showed a differential presence in case and control samples. The disease-associated candidate peptides predicted to be presented by risk HLA proteins contained predominantly aromatic amino acids. In contrast, protective HLA proteins were predicted to bind peptides enriched in acidic amino acids. In summary, we present a proof-of-concept immunogenetic analysis that contributes to a better understanding of the HLA in UC.